I decided to play this hack and to make it more interesting I planned on making a baton pass team. So I caught a ledyba which learned baton pass and breeded it with a scyther. The female scyther that hatched had the move baton pass. When I tried to let that same scyther with baton pass breed with a dustox who had learned silver wind, a scyther hatched with silver wind, but not with the move baton pass which it should've inherited from it's mother scyther with the move baton pass. I should've gotten a scyther with baton pass and silver wind, right?
This kind of ruins my plan on making an unique and fun team I had in mind...

That's NOT odd. In fact, a Pokémon obtained through breeding only inherits moves from its father. So it's impossible in any version that this female Scyther passes Baton Pass to the baby. That's why the hatched Scyther had Silver Wind, but no Baton Pass. Understood?